Myalgic Encephalomyelitis/Chronic Fatigue Syndrome is an idiopathic disabling disorder characterized by persistent, unexplained fatigue in association with impaired memory or cognition, muscle or joint pain, headache, sore throat, tender lymphadenopathy and night sweats. The prevalence in the US is estimated at over 200 cases/100,000 population with annual medical care costs of $24 billion. There is no specific diagnostic test or treatment. Although the majority of cases are sporadic, there are reports of geographic and temporal clusters of CFS and many subjects report a viral prodrome and symptoms consistent with an infection. Efforts to identify causative agents have yielded inconsistent results and in some instances culminated in false leads that polarized the patient advocate and biomedical research communities, led to inappropriate allocation of resources and placed patients at risk for inappropriate therapeutic interventions. This project will test the hypothesis that CFS cases and controls differ with respect to bacterial, fungal or viral microflora in the oropharynx, lower gastrointestinal tract and blood in a well-powered study, using rigorously characterized cases and controls and state-of-the-art methods for microbial surveillance and discovery. Our proposal builds on the foundation established during the NIAID CFS multicenter study of XMRV/pMLV. It includes the expert clinicians who led work at the original six sites, thereby ensuring credibility within the scientific and CFS patient and advocacy communities and access to a network within which follow-up studies and translational research can be readily pursued. The laboratory team has extensive experience in infectious disease epidemiology, microbial discovery and de-discovery, as well as in the development of serological assays and animal models needed to test for causal relationships and investigate pathogenetic mechanisms.